Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

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Comparative analysis of bile acid composition and metabolism in the liver of Bufo gargarizans aquatic larvae and terrestrial adults 水生幼虫和陆生成虫肝脏中胆汁酸组成和代谢的比较分析
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-09-07 DOI: 10.1016/j.cbd.2024.101322
{"title":"Comparative analysis of bile acid composition and metabolism in the liver of Bufo gargarizans aquatic larvae and terrestrial adults","authors":"","doi":"10.1016/j.cbd.2024.101322","DOIUrl":"10.1016/j.cbd.2024.101322","url":null,"abstract":"<div><p>Bile acids are crucial for lipid metabolism and their composition and metabolism differ among species. However, there have been no data on the differences in the composition and metabolism of bile acids between aquatic larvae and terrestrial adults of amphibians. This study explored the differences in composition and metabolism of bile acid between <em>Bufo gargarizans</em> larvae and adults. The results demonstrated that adult liver had a lower total bile acid level and a higher conjugated/total bile acid ratio than larval liver. Meanwhile, histological analysis revealed that the larvae showed a larger cross-sectional area of bile canaliculi lumen compared with the adults. The transcriptomic analysis showed that <em>B. gargarizans</em> larvae synthesized bile acids through both the alternative and the 24-hydroxylase pathway, while adults only synthesized bile acids through the 24-hydroxylase pathway. Moreover, bile acid regulator-related genes <em>FXR</em> and <em>RXRα</em> were highly expressed in adult, whereas genes involved in bile acid synthesis (<em>CYP27A1</em> and <em>CYP46A1</em>) were highly expressed in larvae. The present study will provide valuable insights into understanding metabolic disorders and exploring novel bile acid-based therapeutics.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142161830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Immune response for acute Aeromonas hydrophila infection in two distinct color morphs of northern snakehead, Channa argus 两种不同颜色形态的乌鳢对急性嗜水气单胞菌感染的免疫反应
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-09-07 DOI: 10.1016/j.cbd.2024.101321
{"title":"Immune response for acute Aeromonas hydrophila infection in two distinct color morphs of northern snakehead, Channa argus","authors":"","doi":"10.1016/j.cbd.2024.101321","DOIUrl":"10.1016/j.cbd.2024.101321","url":null,"abstract":"<div><p>To compare and analyze the differences in immunological response between the two color morphs of <em>Channa argus</em>, a fish cohort was divided into four groups: black <em>C argus</em> + PBS (B-PBS), black <em>C argus</em> + <em>Aeromonas hydrophila</em> (B-Ah), white <em>C. argus</em> + PBS (W-PBS), and white <em>C. argus</em> + <em>A hydrophila</em> (W-Ah). The B-PBS and W-PBS groups received 100 μL PBS, while the B-Ah and W-Ah groups received 3.6 × 10<sup>5</sup> CFU/mL <em>A. hydrophila</em> in the same volume. The death rate in each group was noted, changes in plasma biochemical indicators and the expression of liver immune-related genes were examined, and transcriptome techniques were used to compare the differences between the two colors of <em>C. argus</em> following stress. No mortality occurred in the B-PBS and W-PBS groups. Mortality in the W-Ah and B-Ah groups showed an upward and then downward trend after <em>A. hydrophila injection</em>. The highest mortality occurred within 24 h and was higher in the W-Ah group than in the B-Ah group. MDA levels in the B-Ah and W-Ah groups increased and then decreased, while SOD and T-AOC showed the reverse tendency. The W-Ah and W-PBS groups differed significantly in MDA at 3, 12, and 24 h, SOD from 6 to 96 h, and T-AOC between 6 and 48 h. Plasma MDA and T-AOC levels at 12 h and SOD levels at 24 and 48 h differed significantly between the B-PBS and B-Ah groups. In both the W-Ah and B-Ah groups, the expression levels of <em>IL-1β</em> and <em>IL-8</em> in the liver showed a temporal pattern with an initial increase followed by a decrease, reaching peak levels after 24 h, while <em>IL-10</em> showed the reverse pattern. Transcriptome analysis of the liver revealed significant differences between the two <em>C. argus</em> colors. Differential genes in black <em>C. argus</em> were mainly enriched in steroid biosynthesis, glycolysis/gluconeogenesis, and glutathione and propanoate metabolism pathways 24 h after infection. In contrast, differential genes in white <em>C. argus</em> were mainly enriched in pathways such as oxidative phosphorylation, pancreatic secretion, and protein digestion and absorption 24 h after infection. After <em>A. hydrophila</em> infection, white <em>C. argus</em> had higher mortality, more severe oxidative stress and inflammatory responses, and lower antioxidant capacity than black <em>C. argus</em>.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142161944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptome analysis provides new insight into the mechanism of Bombyx mori under zinc exposure 转录组分析为了解蚕在锌暴露下的机理提供了新的视角
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-28 DOI: 10.1016/j.cbd.2024.101320
{"title":"Transcriptome analysis provides new insight into the mechanism of Bombyx mori under zinc exposure","authors":"","doi":"10.1016/j.cbd.2024.101320","DOIUrl":"10.1016/j.cbd.2024.101320","url":null,"abstract":"<div><p>Zinc is a significant source of heavy metal pollution that poses risks to both human health and biodiversity. Excessive concentrations of zinc can hinder the growth and development of insects and trigger cell death through oxidative damage. The midgut is the main organ affected by exposure to heavy metals. The silkworm, a prominent insect species belonging to the <em>Lepidoptera</em> class and widely used in China, serves as a model for studying the genetic response to heavy metal stress. In this study, high-throughput sequencing technology was employed to investigate detoxification-related genes in the midgut that are induced by zinc exposure. A total of 11,320 unigenes and 14,723 transcripts were identified, with 553 differentially expressed genes (DEGs) detected, among which 394 were up-regulated and 159 were down-regulated. The Gene Ontology (GO) analysis revealed that 452 DEGs were involved in 18 biological process subclasses, 14 cellular component subclasses and 8 molecular functional subclasses. Furthermore, the KEGG analysis demonstrated enrichment in pathways such as Protein digestion, absorption and Lysosome. Validation of the expression levels of 9 detoxification-related DEGs through qRT-PCR confirmed the accuracy of the RNA-seq results. This study not only contributes new insights into the detoxification mechanisms mechanism of silkworms against zinc contamination, but also serves as a foundation basis for understanding the molecular detoxification processes in lepidopteran insects.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142148687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of low temperature air exposure and immersion on antioxidant, immune, intestinal flora and metabolome of Chinese mitten crab (Eriocheir sinensis) 低温空气暴露和浸泡对中华绒螯蟹抗氧化、免疫、肠道菌群和代谢组的影响
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-26 DOI: 10.1016/j.cbd.2024.101319
{"title":"Effects of low temperature air exposure and immersion on antioxidant, immune, intestinal flora and metabolome of Chinese mitten crab (Eriocheir sinensis)","authors":"","doi":"10.1016/j.cbd.2024.101319","DOIUrl":"10.1016/j.cbd.2024.101319","url":null,"abstract":"<div><p>The aim of this study was to investigate the effects of immersion on immune enzyme activity, haemolymph index, intestinal microbiome and metabolome of <em>E. sinensis</em> after low temperature air exposure. The results showed that low temperature air exposure induced stress response, which led to hepatopancreas injury and increased membrane permeability, but this situation was reversible and alleviated after immersion. In addition, after exposure to low temperature air, haemolymph metabolism-related substances such as glucose and total cholesterol were significantly different from the initial value (<em>P</em> &lt; 0.05), and gradually returned to the initial level after immersion. The changes of intestinal flora and hepatopancreas metabolism caused by low temperature air exposure did not fully recover after immersion, and its negative effects did not completely disappear. The sequencing results showed that the species composition and diversity of intestinal microorganisms of Chinese mitten crabs were changed after low temperature air exposure and immersion treatment. The relative abundance of <em>Bacteroidetes</em> and <em>Proteobacteria</em> were increased, while the relative abundance of <em>Firmicutes</em> was decreased (<em>P</em> &lt; 0.05). Metabolomics analysis showed that lysine levels increased significantly, taurocholic acid levels decreased significantly, and amino acid metabolism and lipid metabolism balance were disturbed in hepatopancreas of <em>E. sinensis</em> after exposure to low temperature air and immersion (<em>P</em> &lt; 0.05). This study will provide new insights into the recovery mechanism of water immersion on Chinese mitten crabs after exposure to air.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolutionary origin and distribution of leucine-rich repeat-containing G protein-coupled receptors in insects 昆虫中富含亮氨酸重复的 G 蛋白偶联受体的进化起源与分布
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-24 DOI: 10.1016/j.cbd.2024.101318
{"title":"Evolutionary origin and distribution of leucine-rich repeat-containing G protein-coupled receptors in insects","authors":"","doi":"10.1016/j.cbd.2024.101318","DOIUrl":"10.1016/j.cbd.2024.101318","url":null,"abstract":"<div><p>Leucine-rich repeat-containing G protein-coupled receptors (LGRs) are crucial for animal growth and development. They were categorized into four types (A, B, C1, and C2) based on their sequence and domain structures. Despite the widespread distribution of LGRs across bilaterians, a thorough investigation of their distribution and evolutionary history remains elusive. Recent studies insect LGRs, especially the emergence of type C2 LGRs in various hemimetabolous insects, had prompted our study to address these problems. Initially, we traced the origins of LGRs by exploiting data from 99 species spanning 11 metazoan phyla, and discovered that type A and B LGRs originated from sponges, while type C LGRs originated from cnidarians. Subsequently, through comprehensive genomic and transcriptomic analyses across 565 species across 25 orders of insects, we found that both type A and C1 LGRs divided into two gene clusters. These clusters can be traced back to basal Insecta and an early ancestor of the Arthropoda, respectively. Furthermore, the absence of type B LGRs in wingless insects suggests a role in wing development, while the absence of type C2 LGRs in holometabolous insects hints at novel functions unrelated to insect metamorphosis. According to the origin of LGRs and the investigation of LGRs in insects, we speculated that type A and B LGRs appeared first among four types of LGRs, type A evolved into type C LGRs later, and type A and C1 LGRs independently duplicated during the evolutionary process. This study provides a more comprehensive view of the evolution of LGR genes than previously available, and sheds light on the evolutionary history and significance of LGRs in insect biology.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142097271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptome, histology, and enzyme activities analysis of liver in Phoxinus lagowskii to the low temperature stress and recovery 低温胁迫和恢复期豚鼠肝脏转录组、组织学和酶活性分析
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-23 DOI: 10.1016/j.cbd.2024.101317
{"title":"Transcriptome, histology, and enzyme activities analysis of liver in Phoxinus lagowskii to the low temperature stress and recovery","authors":"","doi":"10.1016/j.cbd.2024.101317","DOIUrl":"10.1016/j.cbd.2024.101317","url":null,"abstract":"<div><p>Assessing the response and resilience of fish to low temperatures over different time scales can provide valuable insights into their mechanisms of adaptation to cold conditions. Farmed Amur minnows (<em>Phoxinus lagowskii</em>) frequently encounter low temperatures, especially during winter. However, the specific responses of <em>P. lagowskii</em> to low-temperature stress remain largely unexplored. In this study, we examined serum glucose and cortisol levels, histological changes, enzymes associated with phosphate and carbohydrate metabolism, triglyceride levels, and liver transcriptomics under various conditions: control (CK), short-term cold exposure (6 days, SC), prolonged cold exposure (14 days, PC), and recovery (RY) from cold exposure at 2 °C. Liver vacuolation was observed during short-term cold exposure. Additionally, we analyzed the enzymatic activity related to carbohydrate and lipid metabolism in serum and liver. Liver transcriptomic data revealed that the PPAR signaling pathway and autophagy-related genes were enriched during short-term cold exposure. Carbohydrate metabolism-related pathways, including the AMPK and MAPK signaling pathways, were significantly enriched after prolonged cold exposure. Metabolic pathways such as fat digestion and absorption, glycine, serine, and threonine metabolism, and arginine and proline metabolism were significantly enriched in the recovery group. Rapid warming after prolonged cold stress allowed <em>P. lagowskii</em> to recover quickly. These findings suggest that <em>P. lagowskii</em> has a strong adaptive capacity for energy metabolism during prolonged cold exposure and the ability to recover rapidly from cold stress. A comprehensive examination of the histological, physiological, biochemical, and molecular responses of <em>P. lagowskii</em> to low temperatures is crucial for developing effective strategies for cultivating this species in challenging environments.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proteomic analysis revealed gender-related differences in the skin mucus proteome of discus fish (Symphysodon haraldi) during the parental and non-parental care periods 蛋白质组分析揭示了铁饼鱼(Symphysodon haraldi)在育儿期和非育儿期皮肤粘液蛋白质组的性别差异
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-23 DOI: 10.1016/j.cbd.2024.101314
{"title":"Proteomic analysis revealed gender-related differences in the skin mucus proteome of discus fish (Symphysodon haraldi) during the parental and non-parental care periods","authors":"","doi":"10.1016/j.cbd.2024.101314","DOIUrl":"10.1016/j.cbd.2024.101314","url":null,"abstract":"<div><p>The discus fish, <em>Symphysodon</em> spp., a South American cichlid, has a unique parental care behavior where fry bite on parental skin mucus after hatching. In this study, we used LC-MS/MS technique to compare the skin mucus proteome composition of male or female discus fish during parental and non-parental care periods. By multivariate statistical analysis, we found clear separations between different periods and between different sexes of mucus proteome. Compared with non-parental female fish, parental female fish had 283 up-regulated and 235 down-regulated expressed proteins. Compared with non-parental male fish, parental male fish had 169 up-regulated and 120 down-regulated expressed proteins. The differentially expressed proteins for male fish were enriched in sulfur relay system, mucin type O-glycan biosynthesis and antigen processing and presentation pathways, while those for female fish were enriched in sulfur relay system, steroid biosynthesis and complement and coagulation cascades pathways. During the parental care, both male and female discus showed an enhanced lipid metabolism, producing more phospholipids and cholesterol. The difference is that male discus had increased tricarboxylic acid cycle producing more energy during the parental care, while females produced more nucleotides especially guanylic acid. Our study could provide new insights into the understanding of the unique mucus supply behavior of discus fish based on proteomic change.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142087982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptome mining and expression analysis of ABC transporter genes in a monophagous herbivore, Leucinodes orbonalis (Crambidae: Lepidoptera) 单食性食草动物 Leucinodes orbonalis(蟹科:鳞翅目)中 ABC 转运体基因的转录组挖掘和表达分析
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-22 DOI: 10.1016/j.cbd.2024.101316
{"title":"Transcriptome mining and expression analysis of ABC transporter genes in a monophagous herbivore, Leucinodes orbonalis (Crambidae: Lepidoptera)","authors":"","doi":"10.1016/j.cbd.2024.101316","DOIUrl":"10.1016/j.cbd.2024.101316","url":null,"abstract":"<div><p>Insecticide resistance is a global concern and requires immediate attention to manage dreadful insect pests. One of the resistance mechanisms adopted by insects is through ATP-binding cassette (ABC) transporter proteins. These proteins rapidly transport and eliminate the insecticidal molecules across the lipid membranes (Phase III detoxification mechanism). In the present study, we investigated the potential role of ABC transporter genes in imparting insecticide resistance in field-collected insecticide resistant larvae of eggplant shoot and fruit borer (<em>Leucinodes orbonalis</em>; Crambidae: Lepidoptera). Dose-mortality bioassays against five insecticidal molecules revealed moderate to high levels of insecticide resistance (32.2. to 134.1-fold). Thirty-one genes encoding ABC transporter proteins were mined from the transcriptome resources of <em>L. orbonalis</em>. They were classified under eight sub-families (<em>ABCA</em> to <em>ABCH</em>). Phylogenetic analysis indicated <em>ABCG</em> is the most divergent, composed of nine genes as compared to many other insects. Transcriptome analysis of the insecticide resistant and susceptible strains of <em>L. orbonalis</em> revealed differential expression of 13 ABC transporter genes. The altered expression of these genes was further validated using qRT-PCR. The knockdown studies indicated the involvement of <em>ABCD1</em> and <em>ABCG2</em> genes in chlorantraniliprole resistance in the insecticide-resistant strain of <em>L. orbonalis</em>. This study unveils the additional mechanisms employed by <em>L. orbonalis</em> in resisting insecticide toxicity through accelerated excretion mode. These <em>ABCD</em> and <em>ABCG</em> family genes could be candidate targets in developing genome-assisted pest management strategies in the future.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142097270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptomic analysis provides insights into the immune responsive genes in the Procambarus clarkii hepatopancreas challenged with Vibrio parahaemolyticus 转录组分析有助于深入了解受到副溶血性弧菌挑战的蝲蛄肝胰腺中的免疫反应基因。
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-20 DOI: 10.1016/j.cbd.2024.101315
{"title":"Transcriptomic analysis provides insights into the immune responsive genes in the Procambarus clarkii hepatopancreas challenged with Vibrio parahaemolyticus","authors":"","doi":"10.1016/j.cbd.2024.101315","DOIUrl":"10.1016/j.cbd.2024.101315","url":null,"abstract":"<div><p><em>Procambarus clarkii</em> is an economically important species in China; however, its high mortality rate due to pathogenic bacteria, particularly <em>Vibrio parahaemolyticus</em>, results in significant economic loss. This study aimed to understand the immune response of crayfish to bacterial infection by comparing and analyzing transcriptome data of hepatopancreatic tissue from <em>P. clarkii</em> challenged with <em>V. parahaemolyticus</em> or treated with PBS. Physiological indices (TP, Alb, ACP, and AKP) were analyzed, and tissue sections were prepared. After assembling and annotating the data, 18,756 unigenes were identified. A comparison of the expression levels of these unigenes between the control and <em>V. parahaemolyticus</em> groups revealed 4037 DEGs, with 2278 unigenes upregulated and 1759 downregulated in the <em>V. parahaemolyticus</em> group. GO (Gene Ontology) enrichment analysis shows that the DGEs are mainly enriched in cellular anatomical activity, bindinga and cellular process, enrichment analysis of KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways showed that DGEs were mainly enriched in Base excision repair, Phagosome and Longevity regulating pathway. At the same time, lysosome was also enriched. The phagosome and lysosome pathways play a crucial role in the immune defense of crayfish against <em>V. parahaemolyticus</em> injection that will be highlighted. In addition, the expression levels of six selected immune-related DEGs were measured using qRT-PCR, which validated the results of RNA-seq analysis. This study provides a new perspective on the immune system and defense mechanisms of <em>P. clarkii</em> and a valuable foundation for further investigation of the molecular immune mechanisms of this species.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterization and expression patterns of the Fox gene family under heat and cold stress in Manila clam Ruditapes philippinarum based on genome-wide identification 基于全基因组鉴定的马尼拉蛤蜊 Ruditapes philippinarum 热和冷胁迫下 Fox 基因家族的特征和表达模式
IF 2.2 2区 生物学
Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2024-08-18 DOI: 10.1016/j.cbd.2024.101313
{"title":"Characterization and expression patterns of the Fox gene family under heat and cold stress in Manila clam Ruditapes philippinarum based on genome-wide identification","authors":"","doi":"10.1016/j.cbd.2024.101313","DOIUrl":"10.1016/j.cbd.2024.101313","url":null,"abstract":"<div><p>In this study, the Fox gene family of <em>Ruditapes philippinarum</em> was identified by bioinformatics analysis and genome data. The results showed that a total of 21 Fox genes were identified in <em>R. philippinarum</em>, which were divided into 16 subfamilies, including two members of Foxa subfamily (<em>Foxa1, Foxa2</em>), three members of Foxl subfamily (<em>Foxl1b, Foxl1a, FOXL2</em>), three members of Foxn subfamily (<em>FOXN3, FOX4A, Foxn4b</em>) and one member of other families. The chromosome distribution, domains, conserved motifs, introns, exons and protein tertiary structures of these 21 <em>Fox</em> genes were predicted. By analyzing the RNA-seq data of <em>R. philippinarum</em>, it was found that the Fox gene family was differentially expressed in different tissues, different developmental stages and under heat and cold stress. Most of <em>Fox</em> genes were highly expressed in four tissues: labial palp, gonad, gill and foot. Most of the <em>Fox</em> genes were highly expressed in blastula stage. Most of the <em>Fox</em> genes were highly expressed in high temperature group of two populations, and <em>Foxo</em>, <em>FOXG1</em> were highly expressed in low temperature group. In addition, qPCR showed that the expression levels of <em>Foxo</em> and <em>Foxj1b</em> genes increased significantly under acute cold stress. Therefore, we speculate that <em>Fox</em> genes may play important roles in embryo development and the temperature stress of <em>R. philippinarum</em>, and this study provides a basis for further exploring the molecular mechanism of low temperature tolerance mediated by <em>Fox</em>.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142097269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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